Caloric restriction (CR) can enhance human health, though underlying mechanisms, particularly related to energy expenditure, remain unclear. This ancillary investigation of the only randomized controlled trial of long-term CR in normal-weight adults, aimed to quantify metabolic adaptation following weight loss by assessing changes in energy-expending tissues and organs using magnetic resonance imaging (MRI). Participants in the CR group were prescribed 24-month 25% CR causing a ~ 13% weight loss at 12 months followed by 12 month weight maintenance, whereas the control group maintained ad libitum food intake throughout. The CR group experienced reductions in adipose tissue and skeletal muscle mass compared to the control group. Sleeping energy expenditure decreased more than predicted at 12 months, regardless of whether predictions were based on body mass, dual x-ray absorptiometry (DXA)-derived body composition, or MRI-derived tissue mass. MRI-derived models explained slightly more variation in energy expenditure at baseline and detected greater metabolic adaptation than simpler models based on body mass only. At 24 months, only the models based on DXA and MRI were indicative of persistent metabolic adaptation. These findings highlight the complexity of metabolic responses to CR. Further, advanced imaging techniques hold potential to provide insight into organ-specific contributions to energy metabolism during CR.